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Magnesium in PDB 5i0i: Crystal Structure of Myosin X Motor Domain with 2IQ Motifs in Pre- Powerstroke State

Protein crystallography data

The structure of Crystal Structure of Myosin X Motor Domain with 2IQ Motifs in Pre- Powerstroke State, PDB code: 5i0i was solved by T.Isabet, H.L.Sweeney, A.Houdusse, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.53 / 3.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 113.950, 173.410, 178.750, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 21.9

Other elements in 5i0i:

The structure of Crystal Structure of Myosin X Motor Domain with 2IQ Motifs in Pre- Powerstroke State also contains other interesting chemical elements:

Vanadium (V) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Myosin X Motor Domain with 2IQ Motifs in Pre- Powerstroke State (pdb code 5i0i). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Myosin X Motor Domain with 2IQ Motifs in Pre- Powerstroke State, PDB code: 5i0i:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5i0i

Go back to Magnesium Binding Sites List in 5i0i
Magnesium binding site 1 out of 2 in the Crystal Structure of Myosin X Motor Domain with 2IQ Motifs in Pre- Powerstroke State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Myosin X Motor Domain with 2IQ Motifs in Pre- Powerstroke State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg902

b:69.4
occ:1.00
O A:HOH1006 1.9 72.9 1.0
O1 A:VO4903 1.9 77.4 1.0
O1B A:ADP904 2.0 79.8 1.0
O A:HOH1001 2.1 71.5 1.0
OG1 A:THR164 2.1 78.2 1.0
OG A:SER219 2.3 73.6 1.0
CB A:THR164 3.1 69.4 1.0
PB A:ADP904 3.1 79.3 1.0
CB A:SER219 3.2 67.8 1.0
O3B A:ADP904 3.4 78.5 1.0
V A:VO4903 3.4 77.1 1.0
N A:SER219 3.8 66.8 1.0
O3A A:ADP904 3.9 74.2 1.0
N A:THR164 3.9 63.8 1.0
O3 A:VO4903 4.0 75.6 1.0
OD1 A:ASP434 4.0 0.1 1.0
CA A:THR164 4.1 64.3 1.0
CA A:SER219 4.1 65.0 1.0
CG2 A:THR164 4.2 60.8 1.0
O1A A:ADP904 4.2 73.4 1.0
O2 A:VO4903 4.3 72.3 1.0
O2A A:ADP904 4.4 70.6 1.0
PA A:ADP904 4.4 71.4 1.0
O2B A:ADP904 4.4 78.2 1.0
O4 A:VO4903 4.5 75.2 1.0
OD2 A:ASP434 4.5 0.2 1.0
O A:ASN217 4.5 71.6 1.0
ND2 A:ASN215 4.6 75.0 1.0
CG A:ASP434 4.7 0.1 1.0
C A:SER218 4.9 70.8 1.0
O A:ILE435 4.9 74.9 1.0
CB A:LYS163 4.9 58.4 1.0
C A:LYS163 5.0 65.8 1.0

Magnesium binding site 2 out of 2 in 5i0i

Go back to Magnesium Binding Sites List in 5i0i
Magnesium binding site 2 out of 2 in the Crystal Structure of Myosin X Motor Domain with 2IQ Motifs in Pre- Powerstroke State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Myosin X Motor Domain with 2IQ Motifs in Pre- Powerstroke State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg902

b:0.6
occ:1.00
O B:HOH1001 1.9 80.1 1.0
O1 B:VO4904 1.9 0.4 1.0
O B:HOH1003 1.9 1.0 1.0
OG B:SER219 2.1 0.3 1.0
O2B B:ADP903 2.3 0.8 1.0
OG1 B:THR164 2.3 96.1 1.0
CB B:SER219 3.0 0.2 1.0
CB B:THR164 3.4 0.3 1.0
PB B:ADP903 3.4 0.0 1.0
V B:VO4904 3.5 0.6 1.0
N B:SER219 3.5 0.1 1.0
O3B B:ADP903 3.5 0.7 1.0
CA B:SER219 3.8 0.7 1.0
O3 B:VO4904 4.1 0.3 1.0
OD1 B:ASP434 4.2 0.6 1.0
N B:THR164 4.3 97.1 1.0
CG2 B:THR164 4.3 0.6 1.0
O2A B:ADP903 4.3 0.6 1.0
O2 B:VO4904 4.4 0.2 1.0
O4 B:VO4904 4.4 0.3 1.0
CA B:THR164 4.4 97.5 1.0
O3A B:ADP903 4.4 0.1 1.0
O B:ASN217 4.4 0.6 1.0
O1B B:ADP903 4.6 0.8 1.0
ND2 B:ASN215 4.6 0.1 1.0
OD2 B:ASP434 4.6 0.0 1.0
C B:SER218 4.6 0.3 1.0
ND2 B:ASN209 4.7 0.4 1.0
PA B:ADP903 4.8 0.7 1.0
CG B:ASP434 4.8 0.8 1.0
O1A B:ADP903 4.9 0.5 1.0
C B:SER219 4.9 0.9 1.0
O B:SER219 4.9 0.1 1.0
CA B:SER218 5.0 0.3 1.0

Reference:

V.Ropars, Z.Yang, T.Isabet, F.Blanc, K.Zhou, T.Lin, X.Liu, P.Hissier, F.Samazan, B.Amigues, E.D.Yang, H.Park, O.Pylypenko, M.Cecchini, C.V.Sindelar, H.L.Sweeney, A.Houdusse. The Myosin X Motor Is Optimized For Movement on Actin Bundles. Nat Commun V. 7 12456 2016.
ISSN: ESSN 2041-1723
PubMed: 27580874
DOI: 10.1038/NCOMMS12456
Page generated: Mon Dec 14 20:29:11 2020

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